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Neocortical function and malfunction depends critically on a spectrum of inhibitory interneurons. To gain novel insight in normal brain function and mechanisms leading to diseases, such as epilepsy or schizophrenia, the knowledge about the specific functions of each interneuron type appears crucial. To date, the mystery about the diversity of neocortical interneurons remains still unresolved, even though much effort was devoted to the characterization of mature interneurons in the neocortex. Ten years ago, the discovery of the ganglionic eminence (GE) as origin of neocortical interneurons allowed a novel approach to assess their various identities, and thus prompted researchers to follow the fate of cells accommodated in this region. Despite the knowledge of the source location and its subdivision into three GEs, their molecular identity remained unknown apart from few genes, and consequently unabled the specific isolation of precursor cells. To this purpose, we performed extensive microarray analysis of the three GEs at various developmental timepoints to reveal their molecular heterogeneity and identify novel precursor cell surface markers that would enable their prospective isolation by flow cytometry and subsequent fate assessment in vitro and in vivo. Surprisingly, molecular heterogeneity of the three GEs was restricted to few differentially expressed genes. However, the differences in gene expression became more apparent at late developmental stage that may reflect the increased specification during development. Among the three GEs, the LGE and CGE resembled molecularly each other most, while the MGE and CGE were most distantly related to each other. Furthermore, our genome-wide expression study suggested that the CGE, a structure of so far controversial nature, was rather a unique structure than a fusion of the MGE and LGE. Analysis across developmental timepoints revealed that the MGE underwent tremendous changes in gene expression when compared to the differential expression existing between the homochronic MGE and cerebral cortex. In our microarray screen, we could identify Boc as a novel marker of LGE/CGE-resident precursor cells. Taking advantage of Boc that encodes a cell surface molecule, we could isolate the Boc+ cells from the GE by flow cytometry, and demonstrate that in contrast to Boc– cells, they self-renewed and differentiated into oligodendrocytes, astrocytes, and neurons, and thus identify them as progenitor cells. Furthermore, immunohistochemical studies suggested that Boc+ GE cells may correspond to radial glia, the embryonic neural stem cells. The specific expression of Boc in the LGE and CGE, but not in the MGE during their entire lifetime suggested that Boc is a reliable marker for LGE/CGE-resident precursor cells. To assess the fate of Boc+ GE cells, we performed homotypic transplantations of Boc+ and Boc– cells onto organotypic slice cultures, and observed that in contrast to Boc– cells, Boc+ cells did not migrate from the GE to the neocortex suggesting that Boc+ precursor cells of the GE do not generate neocortical interneurons. In future, additional fate-mapping studies of Boc+ GE cells, such as in vivo transplantation, should shed more light on the ability of Boc+ LGE/CGE precursor cells to generate neocortical interneurons, and dependent on the outcome serve to construct a cell-lineage tree of neocortical interneurons. Thus, Boc will remain a useful tool to investigate developmental processes underlying the generation of neocortical and/or other neurons, such as striatal neurons.